Europe had a long tradition of exploitation of the underclass by the nobility. The conquest of America extended the tradition of becoming landed gentry through conquest. The treatment of the Native Americans was not out of character.
The oppression of the technologically and politically primitive by the technologically and politically powerful (the oppression of the weak by the strong) --- seizure of land and wealth, massacre of the resisters, enslavement of the survivors--- is just about a constant in human history. You'll find it in the history of just about every race, tribe, culture and nation.
The really different thing about the Spanish conquest of the New World was the extent to which there was internal dissent and internal struggle amongst the Spanish, in favor of the rights of the indigenous people and against their enslavement.
It's 6,000 miles from Mesoamerica to Spain --- very difficult miles in the 16th century --- and effective communication, let alone government, from Madrid to Mexico City was very limited and at time spractically impossible. Nevertheless, Queen Isabella and subsequent monarchs tried to curb or limit the enslavement of the indigenous people of the New World.
Theologians at Spanish Universities reasoned that the people of the New World had souls; were created, like all men, in the image and likeness of God; and possessed natural rights, inluding the right to personal liberty. Forceful men like Bartolome de las Casas and Turibius of Mongrovejo spent their lifetimes attempting to protect Indians from the depredations of the Spanish conquistradores: the voice of Spanish Catholic conscience was a constant,and I mean constant challenge and irritant to those in power.
The principles worked out by people like Francisco Vitoria, to try to define just and peaceful relations between Spain and the civilizations she encountered, form the foundation for modern thinking on human rights and international law.
That's what's different about Christian civilization. Not the absence of sin, but the persistent presence of a new level of critical reflection, internal self-criticism and conscience.